NeuroQP Docs

Uploading your data

In the Data view, you can drag and drop files or click Browse files to select images.

File upload happens in two stages: staging and upload.

1. File selection and organization

Selected files show detected animal names, stainings, magnification, AP coordinate, and brain region when required.

At this stage, nothing has been uploaded yet. Review the detected values and fix any issues before starting the upload.

2. Uploading

Once the staged files look correct, click Upload.

Keep the page open until upload completes.

How metadata detection works

From each filename, NeuroQP tries to detect:

  • Animal
  • Staining, including aliases
  • Magnification (4x, 10x, or 20x)
  • AP coordinate
  • Brain region, for Detail only projects

The app matches detected values against your Study setup and the image slots required by the project's acquisition mode and image roles.

Filename best practices

Use predictable filenames that include the key metadata parts.

Recommended structure for registered projects:

  • [Animal]_[Staining]_[Magnification]_AP[-n.nn].ext

Example for a 4x reference + detail 10x project:

FilenameAnimalStainingMagnificationAP coords
M001_DAPI_4x_AP-1.25.tifM001DAPI4x-1.25
M001_DAPI_10x_AP-1.25.tifM001DAPI10x-1.25
M001_cFos_10x_AP-1.25.tifM001cFos10x-1.25

Example for a high-res whole-slice 20x independent marker detection project:

FilenameAnimalStainingMagnificationAP coords
M001_cFos_20x_AP-1.25.tifM001cFos20x-1.25
M001_TRAP_20x_AP-1.25.tifM001TRAP20x-1.25

For Detail only projects, include the intended brain region in the filename when possible, or assign it during staging before upload.

Batch strategy

Instead of uploading hundreds of images at once, it is usually best to upload in multiple batches, for example one animal at a time.

Confirm warnings are resolved before starting large uploads.

Common staging warnings

  • Unknown animal: No animal was detected in the filename.
  • Staining not detected: No configured staining or alias was detected.
  • Magnification not detected: 4x, 10x, or 20x was not detected.
  • AP coordinate not detected: NeuroQP expects a value such as AP-1.25.
  • Brain region not detected: Detail only projects need each slice assigned to a brain region.
  • Missing required role image: A slice is missing an image required by the project acquisition mode and image roles.
  • Duplicate filenames: The filename appears to have been uploaded already.

Critical warnings should be resolved before upload to avoid incomplete processing later.

After upload succeeds, processing starts automatically when prerequisites are available.